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junchaoshi / sports1.1

Small non-coding RNA annotation Pipeline Optimized for rRNA- and tRNA-Derived Small RNAs
GNU General Public License v3.0
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Should the file generated by tRNA_db_processing.pl be used for generating bowtie indexes? #38

Closed SergioRodLla closed 6 months ago

SergioRodLla commented 9 months ago

Hello,

Thank you for developing the tool. I used the provided Mus musculus pre-compiled databases files and I realized they are not the latest release. I want to use the updated files and for that I manually downloaded the mm39-tRNA fasta file. I then saw that you provide a script tRNA_db_processing.pl that adds CCA to 3'end and G to 5'end of Histidine. However, I saw that in the recommended command line you don't indicate the name of the tRNA_CCA index files, even though the bowtie index files are included in the mm10 pre-compiled database:

sports.pl [...] -t /foo/bar/Mus_musculus/GtRNAdb/mm10/mm10-tRNAs Instead of: sports.pl [...] -t /foo/bar/Mus_musculus/GtRNAdb/mm10/mm10-tRNAs_CCA

I wonder what to use with the updated files that I downloaded. Should I pass the *_CCA indexes to sports.pl ?

Thanks,

Sergio

junchaoshi commented 9 months ago

Hi Sergio,

You don't need to pass the *_CCA indexes to sports.pl, as the software will automatically detect them if they are present.

Best regards, Junchao